rs1525402

Variant names:

• chr17-10955347-A-G
• rs1525402

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.226 in 151,996 control chromosomes in the GnomAD database, including 4,048 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.23 (4048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34371 AN: 151878 Hom.: 4043 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.226 AC: 34406 AN: 151996 Hom.: 4048 Cov.: 32 AF XY: 0.230 AC XY: 17109 AN XY: 74294

African (AFR) AF: 0.228 AC: 9442 AN: 41432

American (AMR) AF: 0.310 AC: 4741 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 630 AN: 3466

East Asian (EAS) AF: 0.138 AC: 713 AN: 5160

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4810

European-Finnish (FIN) AF: 0.197 AC: 2090 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.216 AC: 14688 AN: 67950

Other (OTH) AF: 0.226 AC: 478 AN: 2114

Alfa AF: 0.222 Hom.: 15556

Bravo AF: 0.233

Asia WGS AF: 0.215 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.85
DANN	Benign	0.39
PhyloP100		-0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1525402; hg19: chr17-10858664;